Jonathan Dushoff
Professor, Biology

chapters

• Finding Attractors on a Folding Energy Landscape.  572-582. 2011
• Variation in Susceptibility: Lessons from an Insect Virus.  74-84. 2002
• Recent and Historic Red Spruce Mortality: Evidence of Climatic Influence.  319-330. 1986

conferences

• Identifying enterotype in human microbiome by decomposing probabilistic topics into components.  2012 IEEE International Conference on Bioinformatics and Biomedicine. 445-448. 2012
• Incorporating stochasticity in simple models of disease spread.  MODELING PARADIGMS AND ANALYSIS OF DISEASE TRANSMISSION MODELS. 121-133. 2010
• Understanding Nipah virus emergence in peninsular Malaysia: The role of epidemic enhancement in domestic pig populations.  American Journal of Tropical Medicine and Hygiene. 273-273. 2007
• Bursts of non-synonymous substitutions in HIV-1 phylogenetic tree reveal instances of positive selection at conservative protein sites.  PROCEEDINGS OF THE FIFTH INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE, VOL 3. 114-+. 2006

journal articles

• Attenuation of virulence in Yersinia pestis across three plague pandemics.  Science.  388:eadt3880. 2025
• Improved effectiveness of vaccination campaigns against rabies by reducing spatial heterogeneity in coverage..  PLoS Biology.  23:e3002872. 2025
• Reducing spatial heterogeneity in coverage improves the effectiveness of dog vaccination campaigns against rabies..  bioRxiv.  2024.10.03.616420. 2025
• A generalised catalytic model to assess changes in risk for multiple reinfections with SARS-CoV-2..  PLoS ONE.  20:e0315476. 2025
• Examining the molecular clock hypothesis for the contemporary evolution of the rabies virus..  PLoS Pathogens.  20:e1012740. 2024
• Best practices for estimating and reporting epidemiological delay distributions of infectious diseases..  PLoS Computational Biology.  20:e1012520. 2024
• Mathematical modelling for pandemic preparedness in Canada: Learning from COVID-19..  Canada Communicable Disease Report.  50:345-356. 2024
• Incubation Period and Serial Interval of Mpox in 2022 Global Outbreak Compared with Historical Estimates.  Emerging Infectious Diseases.  30:1173-1181. 2024
• The probability of epidemic burnout in the stochastic SIR model with vital dynamics.  Proceedings of the National Academy of Sciences of the United States of America.  121:e2313708120-e2313708120. 2024
• SARS-CoV-2 Incubation Period during Omicron BA.5–Dominant Period, Japan.  Emerging Infectious Diseases.  30:206-207. 2024
• Inferring the differences in incubation-period and generation-interval distributions of the Delta and Omicron variants of SARS-CoV-2.  Proceedings of the National Academy of Sciences of the United States of America.  120:e2221887120. 2023
• Intermediate levels of asymptomatic transmission can lead to the highest epidemic fatalities.  PNAS Nexus.  2:pgad106. 2023
• How time-scale differences in asymptomatic and symptomatic transmission shape SARS-CoV-2 outbreak dynamics.  Epidemics.  42:100664-100664. 2023
• Evaluating undercounts in epidemics: Response to Maruotti et al. (2022).  Journal of Medical Virology.  95:e28474. 2023
• Comparing machine learning approaches to incorporate time-varying covariates in predicting cancer survival time.  Scientific Reports.  13:1370. 2023
• From science to politics: COVID-19 information fatigue on YouTube.  BMC International Health and Human Rights.  22:816. 2022
• The unmitigated profile of COVID-19 infectiousness.  eLife.  11:e79134. 2022
• Testing and Isolation Efficacy: Insights from a Simple Epidemic Model.  Bulletin of Mathematical Biology.  84:66. 2022
• The importance of the generation interval in investigating dynamics and control of new SARS-CoV-2 variants.  Journal of the Royal Society Interface.  19:20220173. 2022
• Increased risk of SARS-CoV-2 reinfection associated with emergence of Omicron in South Africa.  Science.  376:eabn4947. 2022
• The need for linked genomic surveillance of SARS-CoV-2.  Canada Communicable Disease Report.  48:131-139. 2022
• Bounding the levels of transmissibility & immune evasion of the Omicron variant in South Africa 2021
• Age-dependence of healthcare interventions for COVID-19 in Ontario, Canada.  BMC International Health and Human Rights.  21:706. 2021
• Increased risk of SARS-CoV-2 reinfection associated with emergence of Omicron in South Africa 2021
• A shift from science to politics : a content analysis of COVID-19 Videos on YouTube (Preprint) 2021
• Does Counting Different Life Stages Impact Estimates for Extinction Probabilities for Tsetse (Glossina spp)?.  Bulletin of Mathematical Biology.  83:94. 2021
• Transmission dynamics are crucial to COVID-19 vaccination policy.  Proceedings of the National Academy of Sciences of the United States of America.  118:e2105878118. 2021
• The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic.  Current Biology.  31:R918-R929. 2021
• Roles of generation-interval distributions in shaping relative epidemic strength, speed, and control of new SARS-CoV-2 variants 2021
• Speed and strength of an epidemic intervention.  Proceedings of the Royal Society of London. Biological Sciences.  288:20201556. 2021
• A conceptual guide to measuring species diversity.  Oikos.  130:321-338. 2021
• Forward-looking serial intervals correctly link epidemic growth to reproduction numbers.  Proceedings of the National Academy of Sciences of the United States of America.  118:e2011548118. 2021
• Awareness-driven behavior changes can shift the shape of epidemics away from peaks and toward plateaus, shoulders, and oscillations.  Proceedings of the National Academy of Sciences of the United States of America.  117:32764-32771. 2020
• Modifiable factors related to life-space mobility in community-dwelling older adults: results from the Canadian Longitudinal Study on Aging.  BMC Geriatrics.  20:35. 2020
• Acceleration of plague outbreaks in the second pandemic.  Proceedings of the National Academy of Sciences of the United States of America.  117:27703-27711. 2020
• Potential Role of Social Distancing in Mitigating Spread of Coronavirus Disease, South Korea.  Emerging Infectious Diseases.  26:2697-2700. 2020
• Age-dependence of healthcare interventions for SARS-CoV-2 infection in Ontario, Canada 2020
• Reconciling early-outbreak estimates of the basic reproductive number and its uncertainty: framework and applications to the novel coronavirus (SARS-CoV-2) outbreak.  Journal of the Royal Society Interface.  17:20200144-20200144. 2020
• When to be temperate: on the fitness benefits of lysis vs. lysogeny.  Virus Evolution.  6:veaa042. 2020
• Inferring generation-interval distributions from contact-tracing data.  Journal of the Royal Society Interface.  17:20190719-20190719. 2020
• Modeling shield immunity to reduce COVID-19 epidemic spread.  Nature Medicine.  26:849-854. 2020
• The time scale of asymptomatic transmission affects estimates of epidemic potential in the COVID-19 outbreak.  Epidemics.  31:100392-100392. 2020
• Awareness-driven Behavior Changes Can Shift the Shape of Epidemics Away from Peaks and Towards Plateaus, Shoulders, and Oscillations.  medRxiv.  1:2020.05.03.20089524. 2020
• Calibration of individual-based models to epidemiological data: A systematic review.  PLoS Computational Biology.  16:e1007893-e1007893. 2020
• Calibration of individual-based models to epidemiological data: A systematic review.  PLoS Computational Biology.  16. 2020
• Intervention Serology and Interaction Substitution: Modeling the Role of ‘Shield Immunity’ in Reducing COVID-19 Epidemic Spread.  medRxiv.  2020.04.01.20049767. 2020
• Potential roles of social distancing in mitigating the spread of coronavirus disease 2019 (COVID-19) in South Korea.  medRxiv.  1:2020.03.27.20045815. 2020
• The time scale of asymptomatic transmission affects estimates of epidemic potential in the COVID-19 outbreak.  medRxiv.  1:2020.03.09.20033514. 2020
• Traditional Male Circumcision is Associated with Sexual Risk Behaviors in Sub-Saharan Countries Prioritized for Male Circumcision.  AIDS and Behavior.  24:951-959. 2020
• The time scale of asymptomatic transmission affects estimates of epidemic potential in the COVID-19 outbreak 2020
• Patterns of seasonal and pandemic influenza-associated health care and mortality in Ontario, Canada.  BMC International Health and Human Rights.  19:1237. 2019
• Inferring generation-interval distributions from contact-tracing data 2019
• A practical generation-interval-based approach to inferring the strength of epidemics from their speed.  Epidemics.  27:12-18. 2019
• I can see clearly now: Reinterpreting statistical significance.  Methods in Ecology and Evolution.  10:756-759. 2019
• Correction: Male and female bees show large differences in floral preference.  PLoS ONE.  14:e0217714-e0217714. 2019
• Male and female bees show large differences in floral preference.  PLoS ONE.  14:e0214909-e0214909. 2019
• Partner age differences and associated sexual risk behaviours among adolescent girls and young women in a cash transfer programme for schooling in Malawi.  BMC International Health and Human Rights.  18:403. 2018
• Male and female bees show large differences in floral preference 2018
• Healthcare Resource Uses and Out-of-Pocket Expenses Associated with Pulmonary TB Treatment in Thailand.  PharmacoEconomics - Open.  2:297-308. 2018
• Out-of-Pocket Expenditures, Indirect Costs and Health-Related Quality of Life of Patients with Pulmonary Tuberculosis in Thailand.  PharmacoEconomics - Open.  2:281-296. 2018
• Human ectoparasite transmission of the plague during the Second Pandemic is only weakly supported by proposed mathematical models.  Proceedings of the National Academy of Sciences of the United States of America.  115:E7892-E7893. 2018
• Fitting mechanistic epidemic models to data: A comparison of simple Markov chain Monte Carlo approaches.  Statistical Methods in Medical Research.  27:1956-1967. 2018
• Correction to ‘Speciation over the edge: gene flow among non-human primate species across a formidable biogeographic barrier’.  Royal Society Open Science.  5:180736-180736. 2018
• Equivalence of the Erlang Seir Epidemic Model and the Renewal Equation 2018
• Couple serostatus patterns in sub-Saharan Africa illuminate the relative roles of transmission rates and sexual network characteristics in HIV epidemiology.  Scientific Reports.  8:6675. 2018
• Stochastic simulation of multiscale complex systems with PISKaS: A rule-based approach.  Biochemical and Biophysical Research Communications.  498:342-351. 2018
• Two approaches to forecast Ebola synthetic epidemics.  Epidemics.  22:36-42. 2018
• On the origin of obesity: identifying the biological, environmental and cultural drivers of genetic risk among human populations.  Obesity Reviews.  19:121-149. 2018
• Equivalence of the Erlang-Distributed SEIR Epidemic Model and the Renewal Equation.  SIAM Journal on Applied Mathematics.  78:3258-3278. 2018
• Relatedness of the incidence decay with exponential adjustment (IDEA) model, “Farr's law” and SIR compartmental difference equation models.  Infectious Disease Modelling.  3:1-12. 2018
• Patterns of influenza vaccination coverage in the United States from 2009 to 2015.  International Journal of Infectious Diseases.  65:122-127. 2017
• Kaiso is highly expressed in TNBC tissues of women of African ancestry compared to Caucasian women.  Cancer Causes and Control.  28:1295-1304. 2017
• Speciation over the edge: gene flow among non-human primate species across a formidable biogeographic barrier.  Royal Society Open Science.  4:170351-170351. 2017
• Quantifying ethical tradeoffs for vaccine efficacy trials during severe epidemics 2017
• Lysis, lysogeny and virus–microbe ratios.  Nature.  549:E1-E3. 2017
• A double-edged sword: does highly active antiretroviral therapy contribute to syphilis incidence by impairing immunity toTreponema pallidum?.  Sexually Transmitted Infections.  93:374-378. 2017
• Eco-Evolutionary Theory and Insect Outbreaks.  The American Naturalist.  189:616-629. 2017
• Role of pharmaceutical care for self-administered pulmonary tuberculosis treatment in Thailand.  Journal of Clinical Pharmacy and Therapeutics.  42:337-344. 2017
• Fitting mechanistic epidemic models to data: a comparison of simple Markov chain Monte Carlo approaches 2017
• Evidence that promotion of male circumcision did not lead to sexual risk compensation in prioritized Sub-Saharan countries.  PLoS ONE.  12:e0175928-e0175928. 2017
• Epidemiological impact of a syphilis vaccine: a simulation study.  Epidemiology and Infection.  144:3244-3252. 2016
• Stochasticity and the limits to confidence when estimating R0 of Ebola and other emerging infectious diseases.  Journal of Theoretical Biology.  408:145-154. 2016
• Reevaluating Cumulative HIV-1 Viral Load as a Prognostic Predictor: Predicting Opportunistic Infection Incidence and Mortality in a Ugandan Cohort.  American Journal of Epidemiology.  184:67-77. 2016
• The Hayflick Limit May Determine the Effective Clonal Diversity of Naive T Cells.  Journal of Immunology.  196:4999-5004. 2016
• Estimating finite-population reproductive numbers in heterogeneous populations.  Journal of Theoretical Biology.  397:1-12. 2016
• Lytic to temperate switching of viral communities.  Nature.  531:466-470. 2016
• The risk of incomplete personal protection coverage in vector-borne disease.  Journal of the Royal Society Interface.  13:20150666-20150666. 2016
• Bifurcations and Chaotic Dynamics in a Tumour-Immune-Virus System.  Mathematical Modelling of Natural Phenomena.  11:65-85. 2016
• Intrinsic and realized generation intervals in infectious-disease transmission.  Proceedings of the Royal Society of London. Biological Sciences.  282:20152026-20152026. 2015
• The effect of sexually transmitted co-infections on HIV viral load amongst individuals on antiretroviral therapy: a systematic review and meta-analysis.  BMC Infectious Diseases.  15:249. 2015
• Evaluating Ebola vaccine trials: insights from simulation.  The Lancet Infectious Diseases.  15:1134-1134. 2015
• Modeling the effect of HIV coinfection on clearance and sustained virologic response during treatment for hepatitis C virus.  Epidemics.  12:1-10. 2015
• Statistical power and validity of Ebola vaccine trials in Sierra Leone: a simulation study of trial design and analysis.  The Lancet Infectious Diseases.  15:703-710. 2015
• Correction: Estimating the Global Burden of Endemic Canine Rabies.  PLoS Neglected Tropical Diseases.  9:e0003786-e0003786. 2015
• Estimating the Global Burden of Endemic Canine Rabies.  PLoS Neglected Tropical Diseases.  9:e0003709-e0003709. 2015
• Modeling Post-death Transmission of Ebola: Challenges for Inference and Opportunities for Control.  Scientific Reports.  5:8751. 2015
• Reassessment of HIV-1 Acute Phase Infectivity: Accounting for Heterogeneity and Study Design with Simulated Cohorts.  PLoS Medicine.  12:e1001801-e1001801. 2015
• Modelling of OGTT curve identifies 1 h plasma glucose level as a strong predictor of incident type 2 diabetes: results from two prospective cohorts.  Diabetologia.  58:87-97. 2015
• Ebola virus vaccine trials: the ethical mandate for a therapeutic safety net.  The BMJ.  349:g7518-g7518. 2014
• Post-death Transmission of Ebola: Challenges for Inference and Opportunities for Control 2014
• Ebola control: effect of asymptomatic infection and acquired immunity.  The Lancet.  384:1499-1500. 2014
• Analytic Calculation of Finite-Population Reproductive Numbers for Direct- and Vector-Transmitted Diseases with Homogeneous Mixing.  Bulletin of Mathematical Biology.  76:1143-1154. 2014
• Species Abundance, Not Diet Breadth, Drives the Persistence of the Most Linked Pollinators as Plant-Pollinator Networks Disassemble.  The American Naturalist.  183:600-611. 2014
• Exploring links between pH and bacterial community composition in soils from the Craibstone Experimental Farm.  FEMS Microbiology Ecology.  87:403-415. 2014
• Re: "The 'Case-Chaos Study' l Adjunct or Alternative to Conventional Case-Control Study Methodology".  American Journal of Epidemiology.  179:261-262. 2014
• Estimating Initial Epidemic Growth Rates.  Bulletin of Mathematical Biology.  76:245-260. 2014
• Intimate partner violence is associated with HIV infection in women in Kenya: A cross-sectional analysis.  BMC International Health and Human Rights.  13:512. 2013
• Population-level effects of clinical immunity to malaria.  BMC Infectious Diseases.  13:428. 2013
• Patterns of spread of influenza A in Canada.  Proceedings of the Royal Society of London. Biological Sciences.  280:20131174-20131174. 2013
• Inferring the causes of the three waves of the 1918 influenza pandemic in England and Wales.  Proceedings of the Royal Society of London. Biological Sciences.  280:20131345-20131345. 2013
• Effects of mixing in threshold models of social behavior.  Physical Review E.  88:012816. 2013
• Robust estimation of microbial diversity in theory and in practice.  The ISME Journal.  7:1092-1101. 2013
• Extra-couple HIV transmission in sub-Saharan Africa: a mathematical modelling study of survey data.  The Lancet.  381:1561-1569. 2013
• Genomic Dynamics of Transposable Elements in the Western Clawed Frog (Silurana tropicalis).  Genome Biology and Evolution.  5:998-1009. 2013
• Designing Programs for Eliminating Canine Rabies from Islands: Bali, Indonesia as a Case Study.  PLoS Neglected Tropical Diseases.  7:e2372-e2372. 2013
• HIV Sexual Transmission Is Predominantly Driven by Single Individuals Rather than Discordant Couples: A Model-Based Approach.  PLoS ONE.  8:e82906-e82906. 2013
• A non-negative matrix factorization framework for identifying modular patterns in metagenomic profile data.  Journal of Mathematical Biology.  64:697-711. 2012
• Effects of School Closure on Incidence of Pandemic Influenza in Alberta, Canada.  ACP journal club.  156:173-173. 2012
• Agricultural intensification, priming for persistence and the emergence of Nipah virus: a lethal bat-borne zoonosis.  Journal of the Royal Society Interface.  9:89-101. 2012
• Functional Biogeography of Ocean Microbes Revealed through Non-Negative Matrix Factorization.  PLoS ONE.  7:e43866-e43866. 2012
• How to Make Epidemiological Training Infectious.  PLoS Biology.  10:e1001295-e1001295. 2012
• Multi-Stability and Multi-Instability Phenomena in a Mathematical Model of Tumor-Immune-Virus Interactions.  Bulletin of Mathematical Biology.  73:2932-2961. 2011
• The odds of duplicate gene persistence after polyploidization.  BMC Genomics.  12:599. 2011
• Age-specific mortality risk from pandemic influenza.  Journal of Theoretical Biology.  288:29-34. 2011
• Mechanistic modelling of the three waves of the 1918 influenza pandemic.  Theoretical Ecology.  4:283-288. 2011
• Prevalence of Epistasis in the Evolution of Influenza A Surface Proteins.  PLoS Genetics.  7:e1001301-e1001301. 2011
• Modeling the Population-Level Effects of Male Circumcision as an HIV-Preventive Measure: A Gendered Perspective.  PLoS ONE.  6:e28608-e28608. 2011
• Unlocking the forest inventory data: relating individual tree performance to unmeasured environmental factors.  Ecological Applications.  20:684-699. 2010
• Fluctuation domains in adaptive evolution.  Theoretical Population Biology.  77:6-13. 2010
• Reconstructing influenza incidence by deconvolution of daily mortality time series.  Proceedings of the National Academy of Sciences of the United States of America.  106:21825-21829. 2009
• Unsupervised statistical clustering of environmental shotgun sequences.  BMC Bioinformatics.  10:316. 2009
• Initial human transmission dynamics of the pandemic (H1N1) 2009 virus in North America.  Influenza and other Respiratory Viruses.  3:215-222. 2009
• Directionality in the evolution of influenza A haemagglutinin.  Proceedings of the Royal Society of London. Biological Sciences.  276:3035-3035. 2009
• On the Accessibility of Adaptive Phenotypes of a Bacterial Metabolic Network.  PLoS Computational Biology.  5:e1000472-e1000472. 2009
• Avoiding spurious findings of nonrandom social structure in association data.  Animal Behaviour.  77:1381-1385. 2009
• Reproductive status influences group size and persistence of bonds in male plains zebra (Equus burchelli).  Behavioral Ecology and Sociobiology.  63:1035-1043. 2009
• On the use of hemagglutination-inhibition for influenza surveillance: Surveillance data are predictive of influenza vaccine effectiveness.  Vaccine.  27:2447-2452. 2009
• Transmission Dynamics and Prospects for the Elimination of Canine Rabies.  PLoS Biology.  7:e1000053-e1000053. 2009
• Ability to Replicate in the Cytoplasm Predicts Zoonotic Transmission of Livestock Viruses.  Journal of Infectious Diseases.  199:565-568. 2009
• A mixability theory for the role of sex in evolution.  Proceedings of the National Academy of Sciences of the United States of America.  105:19803-19808. 2008
• Host‐Pathogen Interactions, Insect Outbreaks, and Natural Selection for Disease Resistance.  The American Naturalist.  172:829-842. 2008
• Directionality in the evolution of influenza A haemagglutinin.  Proceedings of the Royal Society of London. Biological Sciences.  275:2455-2464. 2008
• SCALING FROM TREES TO FORESTS: TRACTABLE MACROSCOPIC EQUATIONS FOR FOREST DYNAMICS.  Ecological Monographs.  78:523-545. 2008
• WHITE SPRUCE MEETS BLACK SPRUCE: DISPERSAL, POSTFIRE ESTABLISHMENT, AND GROWTH IN A WARMING CLIMATE.  Ecological Monographs.  78:489-505. 2008
• Antibiotic Overuse: The Influence of Social Norms.  Journal of the American College of Surgeons.  207:265-275. 2008
• Exploring reservoir dynamics: a case study of rabies in the Serengeti ecosystem.  Journal of Applied Ecology.  45:1246-1257. 2008
• Natural Selection for Nucleotide Usage at Synonymous and Nonsynonymous Sites in Influenza A Virus Genes.  Journal of Virology.  82:4938-4945. 2008
• Alternative stable states in host–phage dynamics.  Theoretical Ecology.  1:13-19. 2008
• Rabies Exposures, Post-Exposure Prophylaxis and Deaths in a Region of Endemic Canine Rabies.  PLoS Neglected Tropical Diseases.  2:e339-e339. 2008
• Intraspecific Variation and Species Coexistence.  The American Naturalist.  170:807-818. 2007
• Native bees provide insurance against ongoing honey bee losses.  Ecology Letters.  10:1105-1113. 2007
• On State-Space Reduction in Multi-Strain Pathogen Models, with an Application to Antigenic Drift in Influenza A.  PLoS Computational Biology.  3:e159-e159. 2007
• The Genesis and Spread of Reassortment Human Influenza A/H3N2 Viruses Conferring Adamantane Resistance.  Molecular Biology and Evolution (MBE).  24:1811-1820. 2007
• Synchronous cycles of domestic dog rabies in sub-Saharan Africa and the impact of control efforts.  Proceedings of the National Academy of Sciences of the United States of America.  104:7717-7722. 2007
• Vaccinating to Protect a Vulnerable Subpopulation.  PLoS Medicine.  4:e174-e174. 2007
• Epidemic Enhancement in Partially Immune Populations.  PLoS ONE.  2:e165-e165. 2007
• Network metrics reveal differences in social organization between two fission–fusion species, Grevy’s zebra and onager.  Oecologia.  151:140-149. 2007
• Bursts of nonsynonymous substitutions in HIV-1 evolution reveal instances of positive selection at conservative protein sites.  Proceedings of the National Academy of Sciences of the United States of America.  103:19396-19401. 2006
• Codon Usage and Selection on Proteins.  Journal of Molecular Evolution.  63:635-653. 2006
• Estimating Selection Pressures from Limited Comparative Data.  Molecular Biology and Evolution (MBE).  23:1457-1459. 2006
• Estimating selection pressures from limited comparative data.  Molecular Biology and Evolution (MBE).  23:1457-1459. 2006
• Enhancing the Use of Clinical Guidelines: A Social Norms Perspective.  Journal of the American College of Surgeons.  202:826-836. 2006
• Battling bad behavior (vol 20, pg 51, 2002).  SCIENTIST.  20:15-15. 2006
• Erratum: Battling bad behavior (Scientist 20, 2 (51-57)).  SCIENTIST.  20:15. 2006
• A Monte Carlo model for estimating the productivity of a generalist brood parasite across multiple host species.  Evolutionary Ecology Research.  8:213-236. 2006
• Battling bad behavior.  SCIENTIST.  20:51-+. 2006
• US flu mortality estimates are based on solid science.  The BMJ.  332:177.2-178. 2006
• Mortality due to Influenza in the United States—An Annualized Regression Approach Using Multiple-Cause Mortality Data.  American Journal of Epidemiology.  163:181-187. 2006
• Assessing influenza-related mortality: Comment on Zucs et al..  Discover Public Health.  2:7. 2005
• The entomological inoculation rate and Plasmodium falciparum infection in African children.  Nature.  438:492-495. 2005
• Agricultural Antibiotics and Human Health.  PLoS Medicine.  2:e232-e232. 2005
• Agricultural antibodies and human health: Does antibiotic use in agriculture have a greater impact than hospital use?1.  International Journal of Risk and Safety in Medicine.  17:147-155. 2005
• Directed seed dispersal and metapopulation response to habitat loss and disturbance: application toEichhornia paniculata.  Journal of Ecology.  93:658-669. 2005
• MARINE RESERVE DESIGN AND THE EVOLUTION OF SIZE AT MATURATION IN HARVESTED FISH.  Ecological Applications.  15:882-901. 2005
• Testing Simple Indices of Habitat Proximity.  The American Naturalist.  165:707-717. 2005
• Codon volatility does not detect selection (reply).  Nature.  433:E7-E8. 2005
• On state-space reduction in multi-strain pathogen models, with an application to antigenic drift in influenza A.  PLoS Computational Biology.  preprint:e159-e159. 2005
• Dynamical resonance can account for seasonality of influenza epidemics.  Proceedings of the National Academy of Sciences of the United States of America.  101:16915-16916. 2004
• The Risk of a Mosquito-Borne Infectionin a Heterogeneous Environment.  PLoS Biology.  2:e368-e368. 2004
• Synonymous codon usage and selection on proteins 2004
• The combined effects of pathogens and predators on insect outbreaks.  Nature.  430:341-345. 2004
• Comment on "Metapopulation Persistence with Age-Dependent Disturbance or Succession".  Science.  304:684-684. 2004
• Correction.  Proceedings of the National Academy of Sciences of the United States of America.  101:5696-5696. 2004
• Erratum: Persistent colonization and the spread of antibiotic resistance in nosocomial pathogens: Resistance is a regional problem (Proceedings of the National Academy of Sciences of the United States of America (March 9, 2004) 101, 10 (3709-3714)).  Proceedings of the National Academy of Sciences of the United States of America.  101:5696. 2004
• Detecting selection using a single genome sequence of M. tuberculosis and P. falciparum.  Nature.  428:942-945. 2004
• Mangrove filtration of anthropogenic nutrients in the Rio Coco Solo, Panama.  Management of Environmental Quality.  15:131-142. 2004
• Persistent colonization and the spread of antibiotic resistance in nosocomial pathogens: Resistance is a regional problem.  Proceedings of the National Academy of Sciences of the United States of America.  101:3709-3714. 2004
• Evolution and persistence of influenza A and other diseases.  Mathematical Biosciences.  188:17-28. 2004
• A simulation model of African Anopheles ecology and population dynamics for the analysis of malaria transmission..  Malaria Journal.  3:29-29. 2004
• Codon bias and frequency-dependent selection on the hemagglutinin epitopes of influenza A virus.  Proceedings of the National Academy of Sciences of the United States of America.  100:7152-7157. 2003
• Metapopulations, community assembly, and scale invariance in aspect space.  Theoretical Population Biology.  62:329-338. 2002
• Ecology and evolution of the flu.  Trends in Ecology and Evolution.  17:334-340. 2002
• Hemagglutinin sequence clusters and the antigenic evolution of influenza A virus.  Proceedings of the National Academy of Sciences of the United States of America.  99:6263-6268. 2002
• Community assembly and the emergence of ecosystem pattern.  Scientia Marina.  65:171-179. 2001
• EVALUATING THE RISKS OF ENGINEERED VIRUSES: MODELING PATHOGEN COMPETITION.  Ecological Applications.  11:1602-1609. 2001
• Evaluating the Risks of Engineered Viruses: Modeling Pathogen Competition.  Ecological Applications.  11:1602-1602. 2001
• Phenotypic diversity and ecosystem functioning in changing environments: A theoretical framework.  Proceedings of the National Academy of Sciences of the United States of America.  98:11376-11381. 2001
• Community of assembly and the emergence of ecosystem pattern.  Scientia Marina.  65:171-179. 2001
• Pathogen‐Driven Outbreaks in Forest Defoliators Revisited: Building Models from Experimental Data.  The American Naturalist.  156:105-120. 2000
• Carrying Capacity and Demographic Stochasticity: Scaling Behavior of the Stochastic Logistic Model.  Theoretical Population Biology.  57:59-65. 2000
• Host Heterogeneity and Disease Endemicity: A Moment-Based Approach.  Theoretical Population Biology.  56:325-335. 1999
• Local Frequency Dependence and Global Coexistence.  Theoretical Population Biology.  55:270-282. 1999
• Limiting Similarity, Species Packing, and System Stability for Hierarchical Competition‐Colonization Models.  The American Naturalist.  153:371-383. 1999
• Backwards bifurcations and catastrophe in simple models of fatal diseases.  Journal of Mathematical Biology.  36:227-248. 1998
• Incorporating Immunological Ideas in Epidemiological Models.  Journal of Theoretical Biology.  180:181-187. 1996
• Line Intersect Sampling of Forest Canopy Gaps.  Forest Science.  42:131-138. 1996
• The effects of population heterogeneity on disease invasion.  Mathematical Biosciences.  128:25-40. 1995
• Recent and historic red spruce mortality: Evidence of climatic influencee.  Water, Air, and Soil Pollution.  30:319-330. 1986
• La nécessité d’une surveillance génomique liée du SRAS-CoV-2.  Canada Communicable Disease Report.  48:147-155.

posters

preprints

• Best practices for estimating and reporting epidemiological delay distributions of infectious diseases using public health surveillance and healthcare data 2024
• Reassessing global historical ℛ₀estimates of canine rabies 2024
• Estimating epidemiological delay distributions for infectious diseases 2024
• An extended catalytic model to assess changes in risk for multiple reinfections with SARS-CoV-2 2023
• Examining the molecular clock hypothesis for the contemporary evolution of the rabies virus 2023
• Incubation-period estimates of Omicron (BA.1) variant from Taiwan, December 2021–January 2022, and its comparison to other SARS-CoV-2 variants: a statistical modeling, systematic search and meta-analysis 2023
• Immune boosting bridges leaky and polarized vaccination models 2023
• Toward a comprehensive system for constructing compartmental epidemic models 2023
• Evaluating undercounts in epidemics: response to Maruotti et al. 2022 2022
• Intermediate levels of asymptomatic transmission can lead to the highest levels of epidemic fatalities 2022
• A comparison of machine learning methods to predict survival times for cancer patients: Incorporating time-varying covariates 2022
• Inferring the differences in incubation-period and generation-interval distributions of the Delta and Omicron variants of SARS-CoV-2 2022
• How time-scale differences in asymptomatic and symptomatic transmission shape SARS-CoV-2 outbreak dynamics 2022
• From Science to Politics: COVID-19 Information Fatigue on YouTube 2022
• The unmitigated profile of COVID-19 infectiousness 2021
• Testing and Isolation Efficacy: Insights from a Simple Epidemic Model 2021
• pcoxtime: Penalized Cox Proportional Hazard Model for Time-dependent Covariates 2021
• Age-dependence of healthcare interventions for COVID-19 in Ontario, Canada 2020
• Cohort-based approach to understanding the roles of generation and serial intervals in shaping epidemiological dynamics 2020
• Speed and strength of an epidemic intervention 2020
• Reconciling early-outbreak estimates of the basic reproductive number and its uncertainty: framework and applications to the novel coronavirus (SARS-CoV-2) outbreak 2020
• Calibration of individual-based models to epidemiological data: a systematic review 2019
• When to be Temperate: On the Fitness Benefits of Lysis vs. Lysogeny 2019
• I can see clearly now: reinterpreting statistical significance 2018
• A practical generation interval-based approach to inferring the strength of epidemics from their speed 2018
• Patterns of Influenza Vaccination Coverage in the United States from 2009 to 2015 2017
• Surveillance to Establish Elimination of Transmission and Freedom from Dog-mediated Rabies 2016
• Lysis, Lysogeny, and Virus-Microbe Ratios 2016
• Relatedness of the Incidence Decay with Exponential Adjustment (IDEA) Model, "Farr's Law" and Compartmental Difference Equation SIR Models 2016
• Stochasticity and the limits to confidence when estimating R_0 of Ebola and other emerging infectious diseases 2016
• Regulatory vs. helper CD4⁺T-cell ratios and the progression of HIV/AIDS disease 2014
• Effects of mixing in threshold models of social behavior 2013
• Robust estimation of microbial diversity in theory and in practice 2013
• Fluctuation Domains in Adaptive Evolution 2010
• On the accessibility of adaptive phenotypes of a bacterial metabolic network 2009
• Infections are not alike: the effects of covariation between individual susceptibility and transmissibility on epidemic dynamics
• Over a Century of Infectious Disease Surveillance in Canada: Introducing the Canadian Disease Incidence Dataset (CANDID)

presentations

• Interpreting data for acute respiratory infections: What can we infer from viral testing data? 2024
• Transmission intervals in disease modeling 2024